This is the intended functionality -- exactly so you can use the keyboard on your embedded application. A simple ALT-TAB can do the trick. Now your "issue" is probably because you don't have a FULL keyboard available and my problem is that the same way that you're asking for RR to steal focus away, I'll have other people asking for RR NOT to steal the focus away. All I can recommend is for you to assign a shortcut key on the embeded application or use a hot-key application to try and assign a key globally for the simple purpose of simulating ALT-TAB for instance.